Explore

Cell Browser

Interactive single-cell exploration across 100 vertebrates

The BrainStorm Cell Browser is your entry point into the cross-species brain cell atlas. Open any species and explore its cells on a Uniform Manifold Approximation and Projection (UMAP) embedding, inspect cell-type annotations assigned from the 43-cluster atlas, and query gene expression directly. Every interactive view is available on each species detail page, so you can move from genome to cell type to gene in a few clicks.

Browse All Species Read the Guide
100
Species
across all major vertebrate lineages
43
Clusters
the atlas-level annotation layer
492,121
Analysis-Layer Cells
up to 5,000 cells per species
11,578
Orthologous Genes
human-anchored, shared across species
What the Browser Offers

Three Ways In, One Integrated Embedding

Rather than shipping a single monolithic viewer, we place a full interactive explorer on every species detail page. The entire analysis layer was integrated with Harmony and projected with UMAP, and cells cluster by cell type rather than by species origin. From any species you can trace the same cells through three complementary views.

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UMAP Exploration

Explore cells on the Harmony-integrated UMAP embedding of the 492,121-cell analysis layer. Pan, zoom and select to see how cells group by cell type rather than by species, each large cluster spanning a median of 99 of the 100 analysis-layer species.

UMAP Harmony Interactive
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Cell-Type Annotations

Each cell carries a unified annotation assigned from the 43-cluster atlas, built from expert curation of cluster-level marker expression. Across neurons, glia and vascular lineages, 483,837 of the 492,121 analysis-layer cells (98.3%) carry a unified cell-type label.

43 Clusters Curated 98.3%
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Gene Expression View

Query any of the 11,578 orthologous genes and see how its expression maps onto each species embedding. Compare expression across cell types and across species to trace how conserved programs are shared and remodeled throughout the vertebrate brain.

11,578 Genes Expression Cross-Species
How to Start

Pick a Species, Then Dive In

The quickest path is to choose a species from the full catalog on the species page, then open its detail page, where the interactive browser lives. Or jump straight in with a featured species below. Each card links to that species' interactive page.

STEP 01

Choose a Species

Browse all 100 vertebrates on the species page, from fish to mammals to birds and amphibians.

STEP 02

Open Its Detail Page

Each species detail page embeds the full interactive browser with UMAP, annotations and gene expression.

STEP 03

Compare Across Species

Use the comparative view or open multiple species to see how the same cell types are shared across the tree.

New to the atlas? Read the documentation for a full guide to the browser and the analysis layer before jumping in.
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Mammals

Human

Homo sapiens
Open browser
🐹
Mammals

Mouse

Mus musculus
Open browser
🐵
Mammals

Macaque

Macaca mulatta
Open browser
🐟
Fishes

Zebrafish

Danio rerio
Open browser
🐦
Birds

Chicken

Gallus gallus
Open browser
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Amphibians

Axolotl

Ambystoma mexicanum
Open browser

Want a different context for the browser, such as an in-house or public dataset? The full 100-species catalog with filters is on the species page, and the deeper results that sit behind the annotations live in the cell-type pages: neurons, microglia, astrocytes, and oligodendrocytes.

What the Annotations Mean

Reading the 43-Cluster Annotation Layer

Every cell you see in the browser carries a label from the 43-cluster atlas-level annotation. These 43 clusters were assigned to major cell types by expert manual curation of cluster-level marker expression, then applied programmatically across all 100 species and all 492,121 analysis-layer cells. The table summarizes the major-type breakdown of the annotation layer.

Major Cell Type Clusters in the 43-Cluster Layer What These Labels Tell You
Neurons 27 neuronal clusters Excitatory and inhibitory neurons, the most abundant cell group in the annotation.
Astrocytes 2 clusters Homeostatic and reactive glial populations across lineages.
Microglia / CAMs 3 clusters Immune-competent brain cells, further resolved into 20 microglial subsets in dedicated re-clustering.
Oligodendrocytes 3 clusters Myelinating cells, resolved into 11 oligodendrocyte subclusters on re-clustering.
OPC 2 clusters Oligodendrocyte progenitor cells, resolved into 16 OPC subclusters on re-clustering.
Neuroendocrine 1 cluster A dedicated neuroendocrine population in the analysis layer.
Vascular 1 cluster Endothelial and vascular-lineage cells within the brain.
Ambiguous / Mixed 4 clusters Three ambiguous and one mixed-lineage cluster, retained transparently without a single-type call.

In total, 483,837 of the 492,121 analysis-layer cells (98.3%) carry a unified cell-type annotation, with the rest explicitly labeled unannotated so you can always see which cells lack a confident call. Twelve of the 27 neuronal clusters rest on lower-confidence marker evidence and are retained as curated assignments pending orthogonal support; treat those labels as working hypotheses. The full constellation of marker genes for every cell type is listed in the documentation.

Take the Browser for a Spin

Choose a featured species above or open the full catalog, then explore its UMAP, annotations and gene expression. The documentation keeps the browser conventions and the analysis layer in one place.

Browse All Species Comparative View Documentation